[med-svn] [sparta] 03/03: Versioned Build-Depends: python-htseq (>= 0.6.1p1)

[Andreas Tille]

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tille pushed a commit to branch master
in repository sparta.

commit 66de60cb60ab8113ce0f275b36b0ae025f5881be
Author: Andreas Tille <tille at debian.org>
Date:   Wed Aug 3 11:36:27 2016 +0200

    Versioned Build-Depends: python-htseq (>= 0.6.1p1)
---
 debian/control                      |  2 +-
 debian/patches/fix_htseq_call.patch | 28 ++++++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 5b8e90b..6f6ab65 100644
--- a/debian/control
+++ b/debian/control
@@ -22,7 +22,7 @@ Depends: ${python:Depends},
          fastqc,
          trimmomatic,
          bowtie,
-         python-htseq
+         python-htseq (>= 0.6.1p1)
 Description: automated reference-based bacterial RNA-seq Transcriptome Analysis
  SPARTA is a workflow aimed at analyzing single-end Illumina RNA-seq
  data. The workflow combines several tools: Trimmomatic (read
diff --git a/debian/patches/fix_htseq_call.patch b/debian/patches/fix_htseq_call.patch
new file mode 100644
index 0000000..934c0b5
--- /dev/null
+++ b/debian/patches/fix_htseq_call.patch
@@ -0,0 +1,28 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updata: Thu, 28 Jul 2016 15:13:14 +0200
+Description: Deactivated, wanted to see the htseq-count call and learned
+ that a versioned Build-Depends python-htseq (>= 0.6.1p1) is needed
+
+--- a/mapping_and_counting.py
++++ b/mapping_and_counting.py
+@@ -86,12 +86,16 @@ class Mapping_and_Counting(object):
+                 fname = os.path.splitext(mapfile)[0]
+                 strippedmapfile = fname[len('align'):]
+                 if options.verbose:
+-                    subprocess.Popen("./htseq-count --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} ".format(mode=options.mode, stranded=options.stranded, order=options.order, type=options.type, minqual=options.minqual, idattr=options.idattr) + os.path.join(analysislocation, "Bowtie", mapfile) + " " + gff + " > " + os.path.join(analysislocation, "HTSeq", "map" + strippedmapfile + ".sam"), shell=True).wait()
++                    htsc = "htseq-count"
+                 else:
+-                    subprocess.Popen("./htseq-count --quiet --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} ".format(mode=options.mode, stranded=options.stranded, order=options.order, type=options.type, minqual=options.minqual, idattr=options.idattr) + os.path.join(analysislocation, "Bowtie", mapfile) + " " + gff + " > " + os.path.join(analysislocation, "HTSeq", "map" + strippedmapfile + ".sam"), shell=True).wait()
++                    htsc = "htseq-count --quiet"
++
++                htseqcall= htsc + " --mode={mode} --stranded={stranded} --order={order} --type={type} -a {minqual} --idattr={idattr} ".format(mode=options.mode, stranded=options.stranded, order=options.order, type=options.type, minqual=options.minqual, idattr=options.idattr) + os.path.join(analysislocation, "Bowtie", mapfile) + " " + gff + " > " + os.path.join(analysislocation, "HTSeq", "map" + strippedmapfile + ".sam")
++                print "DEBUG:", htseqcall
++                subprocess.Popen(htseqcall, shell=True).wait()
+ 
+         if options.cleanup:
+             for file in os.listdir(os.path.join(analysislocation, "Bowtie")):
+                 subprocess.Popen("rm " + os.path.join(analysislocation, "Bowtie", "{file}".format(file=file)), shell=True).wait()
+ 
+-        return
+\ No newline at end of file
++        return

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